Yes there is a tool called "Base Station Wizard" and it does exactly what is required automatically for either G-858 or G-859 data.
It was originally developed for base stations with GPS so it would be possible to reduce all records to UTC
time. It does process multiple data sets and multiple record types, and replaces the time stamp with the UTC time from the $GPZDA (or $GPGGA) NMEA GPS string.

G-858 and G-859 instruments do not record GPS when set up in the Base Station recording menu. Instead, record your base station data as a Simple Survey. That way GPS will be recorded with the magnetometer data.

Base station wizard is covered in MagMap manual, starting with page 238 (chapter 19).
You can download the manual at:
http://www.geometrics.com/geometrics-products/geometrics-magnetometers/magnetometer-information-and-case-studies/#Manuals